Publications
Preprints
Engelbrecht E., Rodriguez O.L., Shields K., Schultze S., Tieri D., Jana U., Yaari G., Lees W., Smith M.L. and C.T. Watson. Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry. doi: https://doi.org/10.1101/2023.10.23.563321
Kos J.T., Safonova Y., Shields K.M., Silver C.A., Lees W.D., Collins A.M. and C.T. Watson. Characterization of Extensive Diversity In Immunoglobulin Light Chain Variable Germline Genes Across Biomedically Important Mouse Strains. bioRxiv doi: https://doi.org/10.1101/2022.05.01.489089
Mikelov A, Nefediev G, Tashkeev A, Rodriguez OL, Ortmans DA, Skatova V, Izraelson M, Davydov A, Poslavsky S, Rahmouni S, Watson CT, Chudakov D, Boyd SD, Bolotin D. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR. doi: 10.1101/2023.10.10.561703.
Engelbrecht E., Rodriguez O.L., and C.T. Watson. Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation. https://www.biorxiv.org/content/10.1101/2024.03.06.582860v1
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2024
Lees W., Saha S., Yaari G. and C.T. Watson. 2024. Digger: Directed annotation of immunoglobulin and T cell receptor V, D and J gene sequences and assemblies. Bioinformatics https://doi.org/10.1093/bioinformatics/btae144
Collins A.M., Ohlin M., Corcoran M., Heather J.M., Ralph D., Law M., Martínez-Barnetche J., Ye J., Richardson E., Gibson W.S., Rodriguez O.L., Peres A., Yaari G., Watson C.T. and W.D. Lees. 2024. AIRR-C Human IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes. Front Immunol. Volume 14. https://doi.org/10.3389/fimmu.2023.1330153
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2023
Peres A., Lees W.D., Rodriguez O.L., Lee N.Y., Polak P., Hope R., Kedmi M., Collins A.M., Ohlin M., Kleinstein S.K., Watson C.T. and G. Yaari. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Res. https://doi.org/10.1093/nar/gkad603
Rodriguez O.L., Safonova Y., Silver C.A., Shields K., Gibson W.S., Kos J.T., Tieri D., Ke H., Jackson K.J.L, Boyd S.D., Smith M.L., Marasco W.A., and C.T. Watson. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nat Commun 14, 4419
Ford E.E., Tieri D., Rodriguez O.L., Francoeur N.J., Soto J., Kos J.T., Peres A., Gibson W., Silver C.A., Deikus G., Hudson E., Woolley C.R., Beckmann N., Charney A., Mitchell T.C., Yaari G., Sebra R.P., Watson C.T.* and M.L. Smith*. 2023 FLAIRR-seq: A novel method for single molecule sequencing of near full-length immunoglobulin heavy chain repertoires. J Immunol. ji2200825.
Lees W.D., Christley S., Peres A., Kos J.T., Corrie B., Ralph D., Breden F., Cowell L.G., Yaari G., Corcoran M., Hedestam G.B.K., Ohlin M., Collins A.M., Watson C.T., Busse C.E., and The AIRR Community. 2023. AIRR community curation and standardised representation for immunoglobulin and T cell receptor germline sets. Immunoinformatics. 10:100025
Nickerson K.M., Smita S., Hoehn K.B., Marinov A.D., Thomas K.B., Kos J.T., Yang Y., Bastacky S.I., Watson C.T., Kleinstein S.H. and M.J. Shlomchik. 2023. Age-Associated B Cells are Heterogenous and Dynamic Drivers of Autoimmunity. J Exp Med. 220(5):e20221346.
Pennell M., Rodriguez O.L., Watson C.T. and V. Greiff. 2023. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol. 44(1):7-21. doi: 10.1016/j.it.2022.11.001.
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2022
Rodriguez O.L., Silver C.A., Shields K., Smith M.L. and C.T. Watson. 2022. Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta and beta loci. Cell Genomics. https://doi.org/10.1016/j.xgen.2022.100228
Gibson W.S., Rodriguez O.L., Shields K., Silver C.A., Dorgham A., Emery M., Deikus G., Sebra R., Eichler E.E., Bashir A., Smith M.L., and C.T. Watson. 2022. Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes and Immunity. doi: 10.1038/s41435-022-00188-2
Fichtner M.L., Hoehn K.B., Ford E.E., Mane-Damas M., Oh S., Waters P., Payne A.S., Smith M.L., Watson C.T., Losen M., Martinez-Martinez P., Nowak R.J., Kleinstein S.H. and K.C. O'Connor. 2022. Reemergence of pathogenic, autoantibody-producing B cell clones in myasthenia gravis following B cell depletion therapy. Acta Neuropathol Commun. 10(1):154.
Ford M., Hari A., Rodriguez O.L., Xu J., Lack J., Oguz C., Zhang Y., Weber S., Magglioco M., Barnett J., Xirasagar S., Samuel S., Imberti L., Bonfanti P., Biondi A., Dalgard C.L., Chanock S., Rosen L., Holland S., Su H., Notarangelo L., NIAID COVID Consortium, Vishkin U., Watson C.T., and S.C. Sahinalp. 2022. ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data. Cell Syst. 13(10):808-816.e5.
Collins A.M., Watson C.T., and F. Breden. 2022. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol. 100(7):497-506.
Babrak L., Marquez S., Busse C.E., Lees W.D., Miho E., Ohlin M., Rosenfeld A.M., Stervbo U., Watson C.T. and C.A. Schramm; AIRR Community. 2022. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation. Methods Mol Biol. 2453:279-296
Jackson KJL, Kos J.T., Lees W., Gibson W.S., Smith M.L., Peres A., Yaari G., Corcoran M., Busse C.E., Ohlin M., Watson C.T. and A.M. Collins. 2022. A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice. Front Immunol. 13:888555
Safonova Y., Shin S.B., Kramer L., Reecy J., Watson C.T., Smith T.P.L., and P.A. Pevzner. 2022. Revealing how variations in antibody repertoires correlate with vaccine responses. Genome Res. 2022 Apr;32(4):791-804.
Geller A., Shrestha R., Woeste M., Guo H., Hu X., Ding C., Andreeva K., Chariker J., Zhou M., Tieri D., Watson C.T., Mitchell R., Zhang H., Li Y., Martin R., Rouchka R., and J. Yan. 2022. The Induction of Peripheral Trained Immunity in the Pancreas Incites Anti-tumor Activity to Control Pancreatic Cancer Progression. Nat Commun. 13(1):759. doi: 10.1038/s41467-022-28407-4.
Omer A., Peres A., Rodriguez O.L., Watson C.T., Lees W., Polak P., Collins A.M., G. Yaari. 2022. T Cell Receptor Beta (TRB) Germline Variability is Revealed by Inference From Repertoire Data. Genome Med. 14(1):2. doi: 10.1186/s13073-021-01008-4.
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2021
Rodriguez O.L., Sharp A.J., and C.T. Watson. 2021. Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci. PLoS One. 16(12):e0261374
Zhou M, Dascani P, Ding C, Kos JT, Tieri D, Lin X, Caster D, Powell D, Wen C, Watson CT, Yan J. 2021. Integrin CD11b Negatively Regulates B Cell Receptor Signaling to Shape Humoral Response during Immunization and Autoimmunity. J Immunol. 207(7):1785-1797.
Morrissey S.M., Zhang F., Yang C., Wang Z., Hu X., Fox M., Ding C, Zhang H., Guo H., Tieri D., Kong M., Watson C.T., Mitchell R., Huang J. and J. Yan. 2021. Tumor-derived exosomes drive immunosuppressive macrophages in a pre-metastatic niche through glycolytic dominant metabolic reprogramming. Cell Metab. 17:S1550-4131(21)00421-6
Lee J.H., Toy L., Kos J.T., Safonova Y., Fung K., Greenbaum J., Schief W.R., Havenar-Daughton C., Watson C.T.* and S. Crotty*. 2021. Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells.
Peng K., Safonova Y., Shugay M., Popejoy A., Rodriguez O.L., Breden F., Brodin P., Burkhardt A.M., Bustamante C., Cao-Lormeau V-M., Corcoran M.M., Duffy D., Fuentes-Guajardo M., Fujita R., Greiff V., Jonsson V.D., Liu X., Quintana-Murci L., Rossetti M., Xie J., Yaari G., Zhang W., Abedalthagafi M.S., Adekoya K.O., Ahmed R.A., Chang W., Gray C., NakamuraLees Y., W.D., Khatri P., Alachkar H.*, Scheepers C.*, Watson C.T.*, Karlsson Hedestam G.B.* and S, Mangul*. 2021. Diversity in immunogenomics: the value and the challenge. Nat Methods. 18(6):588-591
Kenter A.L.*, Watson C.T.* and J-H. Spille*. 2021. Igh Locus Polymorphism May Dictate Topological Chromatin Conformation and V Gene Usage in the Ig Repertoire. Front. Immunol. https://doi.org/10.3389/fimmu.2021.682589
Morrissey S.M., Geller A.E., Hu X., Tieri D., Cooke E.A., Ding C., Klaes C.K., Cooke E.A., Woeste M., Martin Z.C., Chen O., Bush S.E., Zhange H., Cavallazi R., Clifford S.P., Chen J., Ghare S., Barve S.S., Cai L., Kong M., Rouchka E.C., McLeish K.R., Uriarte S.M., Watson C.T., Huang J. and J. Yan. 2021. A specific low-density neutrophil population correlates with hypercoagulation and disease severity in hospitalized COVID-19 patients. JCI Insight. 10.1172/jci.insight.148435
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2020
Collins A.M., Yaari G., Shepherd A.J., Lees W. and C.T. Watson. 2020. Germline immunoglobulin genes: disease susceptibility genes hidden in plain sight? Curr Opin Syst Biol. (In press)
Rodriguez O.L., Gibson W.S., Parks T., Emery M., Powell J., Strahl M., Deikus G., Auckland K., Eichler E.E., Marasco W.A., Sebra R., Sharp A.J., Smith M.L., Bashir A. and C.T. Watson. 2020. A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus. Front Immunol. (In press)
Alsoussi W.B., Turner J.S., Case J.B., Zhao H., Schmitz A.J., Zhou J.Q., Chen R.E., Lei T., Rizk A.A., McIntire K.M., Winkler E.S., Fox J.M., Kafai N.M., Thackray L.B., Hassan A.O., Amanat F., Krammer F., Watson C.T., Kleinstein S.H., Fremont D.H., Diamond M.S. and A.H. Ellebedy. 2020. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection. J Immunol. (In press)
Christley S., Aguiar A., Blanck G., Breden F., Bukhari S.A.C., Busse C.E., Jaglale J., Harikrishnan S.L., Laserson U., Peters B., Rocha A., Schramm C.A., Taylor S., Vander Heiden J.A., Zimonja B., The AIRR Community, Watson C.T., Corrie B. and L.G. Cowell. 2020. The ADC API: a web API for the programmatic query of the AIRR Data Commons. Front Immunol. (In press)
Ford M., Haghshenas E., Watson C.T. and S.C. Sahinalp. 2020. Genotyping and Copy Number Analysis of Immunoglobin Heavy Chain Variable Genes using Long Reads. iScience. (In press)
Snyder K. E., Pittard C.M., Fowler A. and C.T. Watson. 2020. “Epic-Genetics”: An exploration of pre-service helping professionals’ (mis)understanding of epigenetic influences on human development. Teaching & Learning Inquiry. 8(1):122-137
Do A., Watson C.T., Cohain A., Griffin R., Grishin A., Wood R., Burks A.W., Jones S., Scurlock A., Leung D., Sampson H., Sicherer S., Sharp A.J., Schadt E. and S. Bunyavanich. 2020. Dual transcriptomic and epigenomic study of reaction severity in peanut allergic children. J Allergy Clin Immunol. 145(4):1219-1230
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2019
Busse C.E., Jackson K.J.L., Watson C.T. and A.M. Collins. 2019. A proposed new nomenclature for the immunoglobulin genes of Mus musculus. Front Immunol. 10:2961
Omer A., Shemesh O., Peres A., Polak P., Shepherd A.J., Watson C.T., Boyd S.D., Collins A.M., Lees W. and G. Yaari. 2019. VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Res. 48(D1):D1051-D1056
Lees W., Busse C.E., Corcoran M., Ohlin M., Scheepers C., Matsen F.A., Yaari G., Watson C.T., The AIRR Community, Collins A. and A.J. Shepherd. 2019. OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Res. 48(D1):D964-D970
Watson C.T., Kos J.T., Gibson W.S., Busse C.E., Newman L., Deikus G., Smith M.L., Jackson K.J.L. and A.M. Collins. 2019. A comparison of immunoglobulin IGHV, IGHD and IGHJ genes in wild‐derived and classical inbred mouse strains. Immunol Cell Biol. 97:888-901
Cirelli K.M., Carnathan D.G., Nogal B., Rodriguez O.L., Martin J.T., Upadhyay A.U., Enemuo C.A., Gebru E.H., Choe Y., Viviano F., Nakao C., Pauthner M., Menis S., Reiss S., Cottrell C.A., Smith M.L., Bastidas R., Gibson W., Wolabaugh A.N., Melo A.B., Cosette B., Kuman V., Patel N., Tokatlian T., Menis S., Kulp D.W., Burton D.R., Murrell B., Bosinger S.E., Schief W.R., Ward A.B., Watson C.T., Silvestri G., Irvine D.J. and S. Crotty. 2019. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cell. 177(5):1153-1171.e28.
Castro K., Ntranos A., Amatruda M., Petracca M., Kosa P., Chen E.Y., Morstein J., Trauner D., Watson C.T., Kiebish M.A., Bielekovad B., Inglese M., Sand I.K. and P. Casaccia. 2019. Body Mass Index in Multiple Sclerosis modulates ceramide-induced DNA methylation and disease course. Ebiomedicine. 43:392-410
Hardesty J.E., Wahlang B., Falkner K.C., Shi H., Jin J., Zhou Y., Wilkey D.W., Merchant M., Watson C.T., Feng W., Morris A., Hennig B., Prough R.A. and M.C. Cave. 2019. Proteomic analysis reveals novel mechanisms by which polychlorinated biphenyls compromise the liver promoting diet-induced steatohepatitis. J. Proteome Res. 18(4):1582-1594
Ohlin M., Scheepers C., Corcoran M., Lees W.D., Busse C.E., Bagnara D., Thörnqvist L., Bürckert J.P., Jackson K.J.L., Ralph D., Schramm C., Marthandan N., Breden F., Scott J.K., Matsen E., Greiff V., Yaari G., Kleinstein S.H., Christley S., Sherkow J.S., Kossida S., Lefranc M.P., van Zelm M.C., Watson C.T., and A.M. Collins. 2019. Inferred allelic variants of immunoglobulin receptor genes: a system for their evaluation and documentation. Front Immunol. 10:435
Ntranos A., Ntranos V., He Y., Bonnefil V., Liu J., Kim-Schulze S., He Y., Zhu Y., Brandstadter R., Watson C.T., Sharp A.J., Katz-Sand I. and P. Casaccia. 2019. Fumarates target the metabolic-epigenetic interplay of brain-homing T cells in multiple sclerosis. Brain. 142(3):647-661
Gadala-Maria D., Gidoni M., Marquez S., Vander Heiden J.A., Kos J.T., Watson C.T., O’Connor K.C., Yaari G. and S.H. Kleinstein. 2019. Identification of subject-specific immunoglobulin alleles from expressed repertoire sequencing data. Front Immunol. 10:129
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2018
Hardesty J.E., Wahlang B., Falkner K.C., Shi H., Jin J., Wilkey D., Merchant M., Watson C.T., Prough R.A. and M.C.Cave. 2018. Hepatic signalling disruption by pollutant Polychlorinated biphenyls in steatohepatitis. Cellular Signaling. 18(4):1582-1594
Garg P., Joshi R., Watson C.T., and A.J. Sharp. 2018. A survey of DNA methylation polymorphism in the human genome identifies environmentally responsive co-regulated networks of epigenetic variation. PLoS Genet. 14(10):e1007707
Collins A.M. and C.T. Watson. 2018. Immunoglobulin light chain gene rearrangements, receptor editing and the development of a self-tolerant antibody repertoire. Front Immunol. 9:2249.
Cobb C., Watson C.T., and S.R. Ellis. 2018. Establishing Best Practices for Effective Online Learning Modules: a Single Institution Study. Med Sci Educ. 28:683–691
Barbosa M., Joshi R.S., Garg P., Martin-Trujillo A., Patel N., Jadhav B., Watson C.T., Gibson W., Chetnik K., Tessereau C., Mei H., De Rubeis S., Reichert J., Lopes F., Vissers L.E.L.M., Kleefstra T., Grice D.E., Edelmann L., Soares G., Maciel P., Brunner H.G., Buxbaum J.D., Gelb B.D., and A.J. Sharp. 2018. Identification of rare de novo epigenetic variations in congenital disorders. Nat Commun. 9(1):2064
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2017
Breden F. and C.T. Watson. 2017. Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1. In: Lim T. (eds) Recombinant Antibodies for Infectious Diseases. Adv Exp Med Biol. 1053:245-263. Springer, Cham
Watson C.T.*, Cohain A.T.*, Griffin R.S., Chun Y., Grishin A., Hacyznska H., Hoffman G.E., Beckmann N.D., Shah H., Dawson P., Henning A., Wood R., Burks A.W., Jones S.M., Leung D. Y.M., Sicherer S., Sampson H.A., Sharp A.J., Schadt E.E., and S. Bunyavanich. 2017. Integrative transcriptomic analysis reveals key drivers of acute peanut allergic reactions. NatCommun. 8(1):1943 *Co-first authors
Rubelt F., Busse C.E., Bukhari S.A.C., Bürckert J-P., Mariotti-Ferrandiz E., Cowell L., Watson C.T., Marthandan N., Faison W.J., Hershberg U., Laserson U., Corrie B., Davis M.M., Peters B., Lefranc M-P., Scott J.K., Breden F., The AIRR Community, Luning Prak E.L. and S.H. Kleinstein. 2017. AIRR Community Recommendations for Sharing Immune Repertoire Sequencing Data. Nat Immunol. 18(12):1274-1278
Sandkam B.A., Joy J.B., Watson C.T. and F. Breden. 2017. Genomic environment impacts color vision evolution in a family with visually-based sexual selection. Genome Biol Evol. 9(11):3100-3107
Breden F., Luning Prak E.T., Peters B., Rubelt F., Schramm C.A., Busse C., Vander Heiden J.A., Christley S., Bukhari S.A., Thorogood A., Matsen F., Wine Y., Laserson U., Klatzmann D., Douek D., Lefranc M-P., Collins A.M., Bubela T., Kleinstein S.H., Watson C.T., Cowell L.G., Scott J.K., and T.B. Kepler. 2017. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol. 8:1418
Watson C.T.*, Glanville J.*, and W.A. Marasco*. 2017. The Individual and Population Genetics of Antibody Immunity. Trends Immunol. 38(7):459-470 *Corresponding
Watson C.T.*, Matsen IV F.A., Jackson K.J.L., Bashir A., Smith M.L., Glanville J., Breden F., Kleinstein S.H., Collins A.M., and C.E. Busse*. 2017. Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data". J Immunol. 198:3371-3373 *Corresponding